Uncharted Destiny
by Nemosynne
Summary: Nothing about their lives had been fair growing up. Samuel Drake knew this all too well. But when he met Elizabeth at a youth detention center as a teenager, he never believed she would change his life the way she did. Where it led to? He didn't know at the time. He just knew that what was meant to be, always found its way. Slow updates. SamxOC, some RafexOC *Rating may change*


**D** **isclaimer** : I do not own the Uncharted series.

 _ **A/N** : I've been a fan since the beginning, and followed Nate on all of his adventures. It was one of the best game series I've ever played, and I was incredibly satisfied with the outcome of UC4, but it left me wanting more! I know this isn't the first "what if he had a love interest" story for Sam in this fandom, but nonetheless I decided to try my hand at writing one! I've tried to stick to the timeline as accurately as possible, and hope there will be little to no contradictions in this story. The story will focus on the life of my OC, Elizabeth, and Samuel Drake with occasional appearances from Rafe, Sully and Nate. I hope you enjoy it! I will be busy with school and traveling for the next few months, but I promise to update as often as I can. Monthly, if possible. Reviews are greatly appreciated! :)_

 _This first chapter is a prologue of sorts, and focuses mainly on the life of the two brothers in the orphanage, to get an idea of how Sam grew up and turned out the way he did._

 ****NEW UPDATE**** I'm back, guys! I added some small changes to this chapter as I've reread it and The next chapter is currently being written. Thanks for your patience! I was away a lot longer than I expected but I have an idea on how to move this story forward now and I can't wait to share it with you**

 ****UPDATED AND REWRITTEN****

* * *

 **~Prologue~**

* * *

 **Boston, Massachusetts. 1981.**

 **Saint Francis Boys' Home**

The two young boys sat alone in the long corridor, on a bench near the window. Ten year old Samuel Morgan kicked his feet back and forth steadily over the recently varnished wooden floors. He glanced over at his five year old brother, Nathan, and saw him clinging to a small stuffed animal, looking afraid. Sam moved closer and wrapped an arm around him to comfort him. They had been waiting on that bench anxiously for the last hour as told, while their father had walked into the large meeting room.

Sister Caroline was a lovely young nun who volunteered to stay with the boys. She waited near the door, not speaking much to Sam and Nate, but occasionally glancing over to make sure they were okay.

Scattered, muffled voices could be heard behind the large wooden doors near them. Sam didn't know what was going on, but if the night before had been any indication of what was happening in there, he knew it couldn't be good. Several people had showed up to the house dressed in suits, and carrying briefcases, along with a priest and a nun. All Sam could remember was the mountain of paperwork he saw them present their father. After that, the boys had gone to their rooms and played there until it was all over. He thought back to his mom...confusion overcoming his mind. He didn't understand, and wanted to know the Why behind it all. Their father had been quiet and reclusive the last few days, barely speaking a word to them. And just last night, after all had gone home, he hadn't even taken the time to tuck little Nathan into his bed, Sam recalled.

Sam noticed that Sister Caroline had disappeared down the hall, and heard the large doors slam shut. He looked to his right and noticed their father coming out of the meeting room. His fists were clenched, tears visibly seen on his cheeks. Sam stood up quickly, and began to approach him.

"Dad...?"

The man took a few steps towards him, and looked down at his son. His expression was lacking any emotion, despite the tears.

"Now listen to me, Samuel," the man began, pausing to lift the boys chin up to him. "You take good care of Nate, you hear? Be strong for him. There's somewhere I need to be now, so don't be causing any trouble for the Sisters while I'm away, got it?" his voice was stern.

Sam remained quiet, but nodded. The man patted him twice on the arm and quickly left, not once looking back at either of them.

"What's going to happen to us, Sammy?" Nathan spoke up, realizing their father had left. "Is daddy coming back?"

Sam hugged him, unsure of what to say.

"Yeah, Nate, he just...he just said he had to take care of something." Samuel didn't feel too optimistic about it, but he wanted be positive for his brother's sake.

They sat there a few moments more, watching the nuns go by with children of all ages. Sam suddenly felt lost and all alone in this strange new place, but knew he had to be there for his little brother. The boys didn't say much to each other, and sat there quietly until they saw Sister Caroline approach them, this time with an older man.

"Samuel, Nathan. I'm Father Ryan Duffy." The man introduced himself. He was the man Sam remembered from the night before.

"Welcome to Saint Francis Boys' Home. This will be your new home now, and we have set up living arrangements for you both."

Sister Caroline knelt down next to Nathan, and put a hand on his shoulder. "Everything's going to be alright, child. You'll get to have a new life here, and make friends."

Nathan shook his head, feeling the tears swell up.

"No, I want to go home! I don't want to stay here." he grabbed onto his brothers arm, crying.

Sam looked at Father Duffy, sadness overcoming him.

"My dad isn't coming back, is he..." he said as-a-matter-of-factly, seeing Father Duffy acknowledge him sadly.

"Oh you poor child..." the woman whispered, as she heard Nathan cry. He really had no idea what happened.

It would be the last time they would ever see their father, as he had surrendered them to the state after their mother's suicide. The trial was long and drawn out, but in the end, it would be the best thing for them, their father had decided.

In time, Nathan would come to understand this as he grew older, but for now, Sister Caroline would do her best to make sure he became accustomed to his new home.

Sam, on the other hand, felt angry and hurt. He had so many questions, some he feared would never be answered. He turned to help Father Duffy carry what little belongings they had to their rooms and stayed quiet for the rest of the afternoon.

They were led into a giant room, with steps on both sides leading up to several different locations. To the front of them was a massive cafeteria and kitchen area. The first and second floors were designated to hold the classrooms and the school's massive library and study hall. The third and fourth floors were the boys' dormitories.

Sam was to stay in a dorm at one end of the corridor for boys ages ten through fourteen on the fourth floor; the other hall being for boys fifteen and up.

Nathan was to be placed in another hall down on the third floor, with boys his age and younger. But he was frightened, and had put up a fight, refusing to stay anywhere without his brother. It was then the nuns decided for the boys' sake that the two could room together for the time being. They were placed in a spare room up on the fifth floor where the Sisters resided. This wasn't usually allowed, but given the circumstances, Father Duffy let it go so long as it was a comfort to the boys.

The room they would stay in was well-kept, but somewhat barren. There were two beds, one on each side of the room, and two small windows that overlooked the rooftops of the city. An old dresser was placed at the far end of the room, by a corner wall. A simple looking light hung down from the ceiling, and the boys had put most of their belongings in the large closet, which also contained plenty of extra bedding. The nuns provided them with towels, toiletries, and for Sam, a schedule of his upcoming classes. Sam felt somewhat fearful of what would happen next for them, and the first few nights at the orphanage he had spent many sleepless hours lying awake in bed, often letting Nathan join him in the bed. They both found it comforting, and despite all the sudden changes in the Morgan boys new life, Sam was thankful in the end that they still had each other.

Weeks passed, and soon a few years had gone by as the boys continued to adjust to their new life at the orphanage.

 **-IV-**

Sam, now thirteen, had taken a liking to history books overtime and spent a lot of his free time in the library. It was a place he found peaceful, where he could get away from the days events and drown himself in stories of the past. Sam found this helpful in coping with his anger towards his father. He didn't want to think about why his dad had dumped them there, nor did he quite understand. As he had gotten older, he found himself becoming more and more interested in finding his mother's belongings. He knew his father had sold all of her possessions, but to whom they had been sold to, he didn't know.

It was storming hard when Sam was woken by his brother one night. They had still been sharing that same small room upstairs, and their beds had been moved closer to each other.

"Hey, Sam, are you awake?" eight year old Nathan asked, approaching his bedside. He was holding a tattered, leather bound book in his arms.

Sam yawned, and sat up in his bed feeling a little groggy. "Yeah, Nate, whatcha got there?"

"Well, it's raining out and I can't really sleep, so I wanted to ask if you could read this to me." he asked, holding out the book to him.

Sam took it, and smiled. It was a 1976 edition of _Sir Francis Drake,_ a biography of the famous vice admiral and navigator written by George Malcolm Thomson in 1972. Sam had been reading it earlier that night, just before the Sisters, as he came to address them, issued the 9 PM curfew.

"Let's make a fort and then I'll read it to you!" Sam suddenly suggested, whipping his covers off. He hoped this would get his brother to sleep. He quietly tiptoed over to Nathan's bed and grabbed the pillow and covers, laying them out on the floor near the old wooden dresser in one of the corners. He returned to his bed and did the same. Grabbing one of his long sheets, he placed it over the old dresser and draped it over the standing mirror nearby. He was careful to make as little noise as possible, as he knew at least two of the Sisters would be on night watch.

Sam went into the fort and gestured for Nathan to follow him.

"Here, lay down." Sam patted the spot full of bedding next to him. Nathan nodded and got himself comfortable on the floor.

"What's the book about Sam? I saw you reading it so I wanted to know what it was too." Nathan said, pulling the covers up. Sam moved over next to him, crossing his legs and setting the flashlight upright on the flat wooden surface.

"Well, Nate, it's all about the great Sir Francis Drake and his adventures on the sea. He would relieve Spanish ships of their New World treasures from Santa Domingo to Cartagena to Cadiz in Spain! Some people called him a greedy pirate, but I call him a hero. The- the Robin Hood of his time!" Sam exclaimed in wonderment and admiration. He then opened the book and began with the first chapter. Nathan watched in awe at his brother, who made various expressions while explaining the story to him.

A half hour had passed before Sam stopped for a moment to rest, slipping a finger inside the book. The storm had calmed down by this time and a light rain continued to fall outside which had relaxed them both. Sam turned to look at his brother, who was nearly asleep, and found himself in deep thought. The story had brought back memories of their mother and the stories she had shared with Sam when he was little. Oh, how he missed her...

"Nathan?" he spoke softly.

"Yeah Sam?" he lifted his head up in a bit of haze, with arms still tucked under his pillow.

"Mom always used to tell me stories about this group of pirates when I was little; and how they made off with one of the largest treasures in history! Can you imagine what it would be like to find it!?" he imagined it himself, eyes growing wide. His imagination took him to very strange, wonderful places.

"I wish I could remember more." he sighed bleakly. They both laid there in silence for a few minutes, with just the sound of the pitter patter of rain hitting the window.

"I think- no." Sam stopped. "One day, we're going to get out of here. And then we're going to find mom's journals. Together." Sam stated with a determined voice, clamping one fist together. He vaguely recalled her always writing in them, and knew that was where he could find answers for them both.

"You promise? You promise you won't leave me here, Sam?" Nathan asked.

"I promise, little brother." Sam smiled at him, pulling up Nathan's blanket over his shoulder. Nathan had his eyes closed, but Sam returned to his book reading. This continued on well into the night, when both boys had eventually fallen asleep.

When Nathan reached adulthood later on in life, this would be the first memory he would recall of the first time he had heard the story of the great seafarer Sir Francis Drake.

 **1985.**

The trouble with Sam began when he turned fourteen. By this time, the Morgan brothers had been moved into their respective dormitories on their designated floors, as the Sisters believed it was time for them to start integrating themselves in with the others. Nathan had grown accustomed to it, and found his skill in performing magic tricks, pretending to be a traveling magician. The other kids his age seemed to enjoy the shows he had put on during their free time after dinner, and he was slowly beginning to make a few friends. He even earned a nickname overtime : "Nate the Great".

Samuel, however, had avoided most of the other boys and began to grow a strong dislike for mass and bible retreats. Especially the bible retreats. To him, those week long retreats were the worst kind of punishment, and he disliked being thrown into doing the bible activities set up for them. He often found himself in trouble by the Sisters when he began skipping mass and getting into fights with the other boys.

The first time it happened was on a Monday, about two weeks after his fourteenth birthday, and right after morning mass...

* * *

 _Sam had rushed out quickly from the auditorium and found a quiet spot to do some writing in the study hall when some of the boys his age had approached him._

 _"Hey, Morgan." One of them, Brandon, shouted his named and quickly put his hand over Sam's notebook to get his attention._

 _"What do you want, Brandon?" Sam sighed, clicking his mechanical pencil rapidly._

 _"Got your Latin homework done yet? You owe us from last time."_

 _"I don't have it finished. You know the Sisters would punish us if they knew." Sam explained, attempting to be rational._

 _Brandon laughed at him. "Yeah? So? You promised you'd give us the answers to the Latin homework if we didn't tell Sister Catherine we saw you sneaking out the other night!"_

 _"There's no way I can help you out today. I don't really have time right now, sorry. Maybe tomorrow." Sam apologized, regretting that he ever promised it._

 _Samuel was a top student in their freshman Latin class, and knew that Brandon had struggled a lot with it. But the truth was that he had never liked the boy, and Sam had seen him take advantage of other students before through blackmail, if there was any to be found. The night Sam had been seen by Brandon and his two friends, Sam had attempted sneaking out to look for a route out of the city on the roof. Brandon had threatened to tell the Sisters, but Sam relied on his impulse and blurted out the first thing that had come to his mind._

 _Sam hadn't finished his homework though he had planned on it once he reached the study hall. However, while sitting in Mass, he had come up with a list of places on where their mother's belongings could possibly be, so he had decided to quickly write about it in his notebook, along with her occupation as a historian to track any other leads._

 _He stood up from his chair and began to stuff things into his book bag to hurry out of there, but not before the other boy had snatched the notebook from his hand rudely._

 _"What's this?" Brandon suddenly questioned, flipping through the writings._

 _"That's actually really important, Brandon. Give it back!" Sam said, pleading to him._

 _Brandon furrowed his eyebrows, and showed the other two boys with him the writings in the book._

 _"You liar! You can't get your Latin done but have time to write about a dead woman in your stupid diary!?" the boy mocked him._

 _Sam felt his blood boil, and clenched his fists. "You- You take that back right now!"_

 _"You know she's in hell because she killed herself right? That's what the Sisters say. Some mother you had!" Brandon shouted, throwing the notebook on the floor._

 _That was the final straw for Sam. Without any hesitation he had attacked the boy, and punched him hard in the jaw._

 _A fight ensued as both boys had pulled each other to the floor, both hitting and cursing at one another. Other boys scrambled over to see what was going on, shouting and chanting._

 _"ENOUGH!" a loud, firm voice was heard throughout the room. Two nuns had rushed over. Everyone got quiet quickly, scattering out of the hall and into their classrooms. Sam had been the one on top punching and hitting, cursing him, when two of the nuns ran in to see the commotion. One of them, Sister Maria had yanked Sam off of him, and saw that both boys had bruises. Sam had give Brandon a bloody nose, and Sam's own lip was bleeding._

 _"Samuel Morgan! What an outrageous display of behavior!" Sister Catherine scolded him, crossing her arms. She glanced over at the other boy, shaking her head at him as well._

 _"He started it!" Sam shouted angrily, annoyed that he was the only one being called out._

 _"Not true! He got mad at me because I said I was going to tell the Sisters I saw him sneaking out one night!" Brandon spouted maliciously. It was a blatant lie, but he didn't care, so long as it saved his tail from getting in trouble._

 _"Is this true, Samuel?" the nun raised her eyebrow at him. Sam said nothing at the time and just looked away._

 _"You boys should be ashamed of yourselves with this nonsensical behavior. How disgraceful." Sister Catherine continued reprimanding them both. Sam rolled his eyes, still reeling from the cruel words that had been said to him about his mother._

 _That day, both boys had been sent to the office where they received disciplinary action. Both of them had been grounded to their dorms outside of class and church for one week. However, because Sam had admitted to sneaking out later on, he received further discipline, and was assigned cleaning duty in the cafeteria for two weeks._

 _Eventually, Father Duffy had found time to take Sam aside and have a long talk with him about his behavior one afternoon during his cleaning duties. He wanted to understand the reason for Sam's actions. He knew in his heart that Samuel's motive was most likely anger that had built up towards their father. He had abandoned them as such a young age, and he knew this had greatly affected Sam. He was hurting deep down, and this rebellious behavior had become an unfortunate way of coping for him._

* * *

That man was the only one Sam had ever grown to respect while growing up in that orphanage. He was stern, old with wisdom, and always showed that he truly cared for Samuel and his brother. He never yelled at the boy, but approached him with a fatherly spirit, and always told Sam growing up that he simply wanted the best for them. Sam wanted to obey, but every year it seemed he became more obsessed with getting out of the orphanage with his brother to find their mother's journal.

As Sam got older, the nuns, along with Father Duffy, began finding it more and more difficult dealing with his juvenile antics. By the time he had reached sixteen, Sam had made it a habit of sneaking out at night on a weekly basis, despite numerous warnings and punishment from the nuns. One day Sister Catherine had even caught him smoking on the rooftop in secrecy. The fight he had with her was so bad that Sam had run away for two days before he was apprehended by police because he had been caught trying to steal three hundred dollars from the office inside a gas station. The look of disappointment on Father Duffy's face when he returned to the orphanage had made Sam feel incredibly guilty about his behavior.

It was even worse when Nathan finally saw him. He had gotten so angry with Sam for running away and leaving him behind. Nathan had cried angry tears, and Sam had apologized several times, telling his brother that he was doing this for the both of them. But Nathan didn't buy it. He knew Sam. And he knew that he would do it again. Sam didn't want the guilt, especially now. He knew he had let Nathan down a lot in the last few years because of his actions. His little brother, now a preteen, was growing up fast and Sam didn't want Nathan looking up to a bad role model like him. But this urge he had to go out and explore...he just couldn't help himself.

 **1988.**

Things took a turn for the worst when Samuel turned seventeen.

Because he was nearing adulthood, he had been able to find a part time job at a nearby restaurant, mostly serving as a dishwasher, when he was not in school.

 _"Definitely a dream job"_ he had joked to himself while being hired. It paid very little, and Sam had grown frustrated with the slow progression of things. To make matters more unbearable, he was annoyed with bad co-workers and sleazy management. It took a downhill spin when he got in trouble one day for smoking in the back of the building during a break. He had been doing it for a while, but had finally been caught. The management had scolded him for his behavior, and Sam left his job after only three months because he could no longer take it.

However, despite his feelings on it being a shitty place to work, he knew it was doing financially well. His last day there he had recalled seeing one of the supervisors in the back with a huge booklet of cash, which would be counted out and marked in a binder before being taken to the bank the next day. That was yesterday, and he knew the money would be there again tonight. He wanted out of this city, along with his brother. It was a risk he knew he had to take.

That night, during a heavy rainfall, Samuel had decided to sneak out once more. He had come up with a plan to steal some cash, return to the orphanage to retrieve Nathan, and leave that place together. For good.

He arrived at the restaurant, which had appeared to be closed for the night. He quickly rushed to the back of the building to get to the employee door. By this time the rain had let up, but Sam was still wet and decided to discard his soaked, muddy shoes and jacket to help prevent extra noise. Retrieving a small set of pins from his jean pocket that he had tediously put together with a pair of pliers, he then proceeded to carefully pick the door's lock. For the next few minutes he moved the lock pick around until he had finally heard the clicking sound he was waiting to hear.

Sam poked his head into the dark restaurant, taking a quick peek around before entering. He slid a rock into the door's entrance to help for a quick escape before heading to the back room. The office door also appeared to be locked. He let out a sigh, rubbing his hands together in sweat. Getting on his knees, he once again stuck the lock pick into the door's lock until it opened. He slowly opened the door, and let out a deep breath. The safe was under the desk, with a binder on top of it. Sam rubbed his hands together, and paused for a moment, asking himself if he was really doing this.

He shrugged off the feeling. He couldn't let guilt get in the way of his goals. Not now. He flipped on the desk lamp and sat in the chair, leaning over to grab the binder. If he was a business man, the most logical place for a code to be kept would be in one of these, securely hidden away under documents. He flipped through the pages, and had let out a yawn.

He glanced down to his wristwatch and sighed.

 _Nearly 2 am._

"Damnit!" he shouted. This was going nowhere fast and he found himself frustrated. The clock was ticking the night away. But just as he had closed the binder, Sam had looked down near his foot as he had spotted something. There, a small note card lay hidden. He picked it up, and sure enough, there was a five digit code to the safe that had been jotted down sloppily with a permanent marker. He silently cursed at himself for not being more observant.

Sam wiped sweat from his brow and kneeled down to the safe to begin unlocking it.

The safe opened, and he felt his heart race. The money was sitting there in a bag, right in front of him. He reached out his hand to take it, but suddenly found himself hesitating as he picked it up.

 _What am I doing? Have I really stooped this low?_

Thoughts whirled through his mind as he stared at the money. He hated this place. He wanted to leave. He had made that promise to Nathan. But Sam never thought he would go to these lengths to fulfill that promise.

Sam shook his head, letting the feeling of shame overcome him and put the money back. He was disappointed in himself; but he knew this wasn't worth it.

 _Another night I guess._

He let out a loud groan and stood up after locking up the safe again. Now he just had to leave this place as quickly as he came.

- **IV-**

It had stopped raining, and still considerably dark out. Sam shut the office door behind and began to head out the back from where he entered. He was hoping to make it back to the orphanage before anyone caught wind of what he had been doing. In the back of his head, he was quietly cursing himself for 'wussing' out, as he had always called it. He just had a strong feeling that tonight was not the right not to leave.

He had almost reached the back employee door when he was startled by bright colorful flashing lights.

"Shit!" he gasped under his breath. Had he been followed!? Without a moment's hesitation he booked it out and began to run. However, upon exiting he was greeted by three officers who immediately grabbed hold of him.

"I didn't take anything! I swear!" Sam shouted as he struggled. A police officer had silenced him and shouted. Sam found himself pummeled to the ground, his hands going behind his back and into cuffs. Looking up, he spotted a very disappointed and saddened Father Duffy standing off in the distance, with his eyes locked onto Sam's own eyes.

This time Sam had been taken to the police station, and placed in a holding cell until further paperwork was done. His heart beat quickly when he saw Father Duffy and Sister Catherine arrive with them in the vehicle. It was nearing 3 am and he knew this wasn't going to be good as they had began conversing with the officers.

After a near half hour of conversation, Father Duffy had approached Sam and took a seat next to him in the cell.

"I was the one that called it, Samuel. We gave you another chance." Father Duffy spoke sternly. "As one of the older students in the home, we expect you to set an example for the younger ones to look up to, and I've got to say, I am so disappointed in you. We can't let this behavior continue, so the orphanage has agreed to send you to the youth detention center downtown, in hopes that it will help you change, Samuel."

Hearing this had upset Sam immensely, but he knew it wouldn't be worth it to fight. He didn't take anything, that was true, but he had broken into it, and he knew Father Duffy was right. There was no justifying it. The nuns had even told Sam just days before that they were giving him one more chance to change his ways and hearing the tone in Father Duffy's voice had made it even worse.

"Why, Samuel..." he had asked softly. He had taken his hat off, holding it in one hand and his overcoat in the other arm. "You are a brilliant student and an intelligent young man. There is so much potential that I see in you. I don't understand why you seem so eager to throw your life away."

The question did not merit a response, but it was something that Sam had definitely thought about. The last thing he wanted was to be stuck at a juvenile center, but he knew he deserved it. He also knew Nathan wouldn't be happy once he found out about it, but Sam figured Nathan would probably be more upset that Sam had, once again, screwed up trying to get them out.

After his court hearing, Sam was sent to the detention center, with the agreement that if he did enough community service and anger management classes, he could be released after 4 months. Of course had had argued that he did not need anger management classes. But the judge had lectured him, and said it was necessary due to his delinquent activities. The stories the judge had heard from the nuns did not help his situation, so Sam had remained quiet the rest of his sentencing, accepting his fate.

Word about Sam's whereabouts eventually got to eleven year old Nathan. He was angry, but not surprised. He had tried telling Sam numerous times what would happen if he had been caught stealing again, but he hadn't listened. With Nathan, the Sisters had tried even harder to see that he wouldn't follow in his brothers footsteps, and so far, things seemed to be going well. And now Nathan was the one that had to stay strong; but this time, for himself. For now, all Nate could do was focus on his studies and remember the promise Sam had made to him when they were younger that they would leave this place together and find their mom's journal.

Life has a strange way of working, and for Sam, though he didn't know it yet, things would never be the same for him from here on out.

* * *

 ** _"It is strange, but true, that the most important turning-points of life often come at the most unexpected times and in the most unexpected ways."_**

 _— Napoleon Hill_


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